get_collectri error

[t1nnenissen]

Hi there,

I have previously been successfully used DecupleR (and I love it!). However, yesterday I ran into an issue.

Running the command:

net <- get_collectri(organism='human', split_complexes=FALSE)

I got the following error:

Do you have idea what that might be due to? My decouple version is 2.7.1 and Omnipath is 3.9.8.

Best, Tinne

[PauBadiaM]

Hi @t1nnenissen

Thanks for opening this issue. @deeenes the right versions look alright, any idea what could be causing it?

[t1nnenissen]

Hi there,

I got another error message not - maybe this can give an better idea of what's happening!

[t1nnenissen]

@deeenes any ideas?

[deeenes]

Hello,

The first post is a bit contradictory for me, because it says static_table is not exported, while the version is 3.9.8, and in that version it was already exported.

In the next log we see that downloading something from omabrowser.org gives the same bad value error. It suggests that likely any call to read_tsv triggers the error. The alternative is that there is something common downstream and we see this error twice just by accident. But let's stay at the first version. Could you please try if the same error manifests when calling read_tsv directly?

library(readr)

example_url <-
    paste0(
        'https://omnipathdb.org/interactions?',
        'genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B',
        '&fields=evidences,sources,references,curation_effort&license=academic'
    )

result <- read_tsv(example_url, col_types = cols(), progress = FALSE)

If you see the error, please show us the traceback.

Also if the error pops up with read_tsv, let's check further: readr::read_tsv calls httr if an URL is provided, httr is built on curl. What happens if you call directly httr::GET or curl::fetch_disk?

library(httr)
library(curl)

resp <- httr::GET(example_url)
resp <- curl::curl_fetch_disk(example_url, tempfile())

bad value errors are unfortunately cryptic, it's difficult to find their reason: it can be running out of memory, null pointer, stack overflow, etc. (Just to make sure: do you run R with plenty of memory available? Though I don't think that's a likely reason, these datasets are not so big.) It would be helpful to see the output of sessionInfo on your machine, after loading OmnipathR:

library(OmnipathR)
sessionInfo()
sessioninfo::session_info()

Also, can you confirm if the packages readr, vroom, httr and curl are all up-to-date?

If this error persists in a reproducible manner, one next step could be to run R with debugger (gdb).

Best, Denes

[t1nnenissen]

Hi Denes,

Thanks a lot!

The issue is resolved now - I think it was due to an issue with the data.table package on my Mac!

Best, Tinne